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Type boolean and numeric parameters and require Nextflow 26.04.6 - #359

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feat/typed-scalar-parameters
Oct 25, 2026
Merged

Type boolean and numeric parameters and require Nextflow 26.04.6#359
nictru merged 3 commits into
devfrom
feat/typed-scalar-parameters

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@nictru

@nictru nictru commented Oct 25, 2026 •
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Summary

Add native boolean and numeric parameter validation without changing analysis interfaces or config defaults, following the metatdenovo approach.

 main.nf
+ params { /* 50 Boolean, Integer and Float declarations, without defaults */ }
 nextflow.config
  params { /* all 111 defaults retained */ }
- nextflowVersion = '!>=25.10.4'
+ nextflowVersion = '!>=26.04.6'

String parameters and boolean-or-string help remain untyped. No workflow/process static typing, plugin upgrades or vendored changes. Update the blocking CI floor, documentation and generated RO-Crate metadata.

Evidence

  • Before: No native scalar declarations in main.nf.
    After: All 50 declarations match schema scalar types and config nullability; a comparison confirms that all 111 defaults remain unchanged.
  • Nextflow 26.04.6: all 12 tests in tests/params.nf.test --profile docker pass. Coverage includes CLI boolean flags, numeric values, nullable parameters, precedence, help/version and native invalid-type errors with schema validation disabled.
  • prek run --all-files and staged pre-commit checks pass.
  • Existing pipeline, local-module and local-subworkflow checks were attempted. Container tasks fail before analysis with Docker/OCI mount permission errors under both the repository and temporary work directories. These runs were interrupted by the command timeout; no snapshots were regenerated.
  • Default-profile CLI regression rerun also passes all 12 tests on Nextflow 26.04.6 in CI mode.
  • All 89 GitHub checks pass for head 11b72771a4b92dca63a49d43a1625f0f11f51f2b, including nf-core lint, pre-commit and all pipeline/module/subworkflow shards on Nextflow 26.04.6 and latest-everything.
  • main.nf retains its original layout outside the typed parameter block. The additional parameter-type usage section was removed at the author's request.

Merge Danger

Door: two-way

Revert the commit to restore the previous declarations and minimum version. No data migration.

Blast Radius: pipeline

All invocations require Nextflow 26.04.6 or later. Invalid scalar values now fail before initialisation, even with --validate_params false. Analysis behaviour and publication paths are unchanged by the implementation, but container-based regression verification remains blocked locally.

Generated by GPT-6.1 Sol

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.
  • README.md is updated.

No new tools, test datasets or output formats are introduced.

@nictru
feat: type boolean and numeric pipeline parameters
a08e296 
Retain config defaults and add CLI regression coverage. Require Nextflow 26.04.6 and update CI, documentation and generated metadata.

Generated by GPT-6.1 Sol
@github-actions

github-actions Bot commented Oct 25, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.1.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Oct 25, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 11b7277

+| ✅ 328 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in CHANGELOG.md: ## v0.0.1dev - [unreleased replace with date on release ]
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-25 09:03:24

nictru added 2 commits October 25, 2026 09:20
@nictru
test: assert help exits before software version publication
b974b6b 
The nf-core content linter requires software-version coverage in pipeline tests. Assert that help-only parameter tests do not publish analysis versions, rather than launching tasks or disabling the lint check.

Generated by GPT-6.1 Sol
@nictru
style: minimise main script template deviations
11b7277 
Restore the existing main.nf layout outside the typed parameter block and remove the additional parameter-type usage section.

Generated by GPT-6.1 Sol
@nictru
nictru marked this pull request as ready for review October 25, 2026 09:33
@nictru
nictru merged commit a2b0a84 into dev Oct 25, 2026
90 checks passed
@nictru
nictru deleted the feat/typed-scalar-parameters branch October 25, 2026 09:33
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@nictru